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IDInstitute: Covid-19 Data Science

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Chonnam National University
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Covid-19 Data Science

Ardiansyah, S.T., M.Eng

Peneliti SDA (Sensor, Data, and AI)

PhD Candidate, Chonnam National University, Korea
Data Science for Covid-19 Indonesia (DSCI) Initiative

https://ardiansyah.id/
email: ardi@ejnu.net
Konten

Covid-19: Situasi Terkini

Jenis & Tipe Data Covid-19

Data, So What?

Data Science for Covid-19

Indonesia
Covid-19: Situasi Terkini
Covid-19 Situasi Terkini

Source: https://www.worldometers.info/coronavirus/
Covid-19 Situasi Terkini
JEnIS & TIPE DATA Covid-19
Epidemiological Data

Worldwide level data

❑Novel Coronavirus COVID-19 (2019-nCoV) Data Repository by Johns Hopkins CSSE
https://github.com/CSSEGISandData/COVID-19

https://www.kaggle.com/sudalairajkumar/novel-corona-virus-2019-dataset

❑ Coronavirus Source Data – WHO Situation Reports

https://ourworldindata.org/coronavirus-source-data

❑ Worldometers Covid-19 Coronavirus Outbreak

https://www.worldometers.info/coronavirus/
Epidemiological Data

Country level data

❑ South Korea - https://www.kaggle.com/kimjihoo/coronavirusdataset

❑ Italy - https://www.kaggle.com/sudalairajkumar/covid19-in-italy

❑ Brazil - https://www.kaggle.com/unanimad/corona-virus-brazil

❑ USA - https://www.kaggle.com/sudalairajkumar/covid19-in-usa

❑ France - https://www.kaggle.com/lperez/coronavirus-france-dataset

❑ Tunisia - https://www.kaggle.com/ghassen1302/coronavirus-tunisia

❑ Japan - https://www.kaggle.com/tsubasatwi/close-contact-status-of-corona-in-japan
Virological Data

➢ Repository of Coronavirus Genomes

https://www.kaggle.com/paultimothymooney/repository-of-coronavirus-genomes

Related publications:

Wu, F., Zhao, S., Yu, B. et al. A new coronavirus associated with human respiratory disease in China. Nature (2020).
https://doi.org/10.1038/s41586-020-2008-3

Zhou, P., Yang, X., Wang, X. et al. A pneumonia outbreak associated with a new coronavirus of probable bat origin.
Nature (2020). https://doi.org/10.1038/s41586-020-2012-7

Chen L, Liu W, et al. RNA based mNGS approach identifies a novel human coronavirus from two individual
pneumonia cases in 2019 Wuhan outbreak. Emerging Microbes & Infections. (2020)
10.1080/22221751.2020.172539
Medical/Health Informatics Data

➢ COVID-19 Chest X-ray Image Dataset

https://github.com/ieee8023/covid-chestxray-dataset

• A database of COVID-19 cases with chest X-ray or CT images that extracted from several publications.

Note

• In late January, a Chinese team published a paper detailing the clinical and paraclinical features of COVID-19.

• They reported that the Covid-19 patients present abnormalities in chest CT images

• Bilateral multiple lobular and subsegmental areas of consolidation constitute the typical findings in chest CT images of intensive care
unit (ICU) patients.

• In comparison, non-ICU patients show bilateral ground-glass opacity and subsegmental areas of consolidation in their chest CT images.
Social Network Data

Coronavirus (covid19) Tweets

• This dataset contains the Tweets of users who have applied the following hashtags: #coronavirus,
#coronavirusoutbreak, #coronavirusPandemic, #covid19, #covid_19

• Data generation tool: CRAN Rtweet package

• https://www.kaggle.com/smid80/coronavirus-covid19-tweets
Published Papers Data

• WHO Database of publications on coronavirus disease (COVID-19)

https://www.who.int/emergencies/diseases/novel-coronavirus-2019/global-research-on-novel-coronavirus-2019-ncov

• Cord-19 Dataset

https://pages.semanticscholar.org/coronavirus-research

CORD-19 is a resource of over 24,000 scholarly articles, including over 12,000 with full text, about COVID-
19, and the coronavirus group. This freely available dataset is provided to the global research community
to apply recent advances in natural language processing and other AI techniques to generate new insights
in support of the ongoing fight against this infectious disease.
Data, So WHAT?
Measure how far & how fast will the Covid-19 pandemic spread

Recommended article:
Source: https://www.kaggle.com/andrearomani/covid-19-predictions-for-serbia
https://www.wired.com/story/how-fast-does-a-virus-spread/
Case Network Graph Visualization and Analysis

Source: https://co.vid19.sg/cases
Predicting which cities should be carefully monitored!

Cities have models with relatively high coefficients which

means more infections could happen as time goes on.

Source: https://www.kaggle.com/sungguni/next-cities-besides-daegu-and-gyungsangbuk-do
 Genome Sequences Analysis

According to Wu 2020, Chen 2020, and Zhou 2020, SARS-CoV-2 should:

• Be represented in GenBank MN908947, MN988668 and MN988669

• Have a nucleotide identity of 89.1% with a bat SARS-like coronavirus (CoV) isolate—bat SL-CoVZC45 (GenBank accession number MG772933)

• Share 79.5% sequence identity to SARS-CoV BJ01 (GenBank accession number AY278488)

Source:
https://www.kaggle.com/paultimothymooney/explore-coronavirus-sars-cov-2-genome
https://www.kaggle.com/paultimothymooney/sequences-of-genomes-similar-to-sars-cov-2
X-Ray Images Analysis for Detecting Covid-19

https://www.linkedin.com/pulse/deteksi-covid-19-menggunakan-computer-vision-dan-deep-siadari

https://github.com/ieee8023/covid-chestxray-dataset
#FlattenTheCurve

https://www.vox.com/2020/3/10/21171481/coronavirus-us-cases-quarantine-cancellation
 COVID-19 Open Research Dataset Challenge (CORD-19)
List of Tasks...
1. What is known about transmission, incubation, and
environmental stability?
2. What do we know about COVID-19 risk factors?
3. What do we know about virus genetics, origin, and evolution?
4. What has been published about ethical and social science
considerations?
https://www.kaggle.com/allen-institute-for-ai/CORD-19-research-challenge
5. What do we know about diagnostics and surveillance?
6. What has been published about medical care?
7. What has been published about information sharing and
inter-sectoral collaboration?
8. What do we know about non-pharmaceutical
interventions?
9. What do we know about vaccines and therapeutics?
Data Science for
Covid-19 Indonesia
Portal Informasi Covid-19 di Indonesia
❑ Aplikasi Satu Data Kementerian Kesehatan

https://data.kemkes.go.id/data/dhis-web-dashboard/#/

❑ BNPB Situasi Virus Corona Nasional

https://www.covid19.go.id/situasi-virus-corona/

❑ Kawal Covid-19 Indonesia

https://kawalcovid19.id/

❑ DKI Jakarta https://corona.jakarta.go.id/

❑ Jawa Barat https://pikobar.jabarprov.go.id/
❑ Jawa Tengah https://corona.jatengprov.go.id/
❑ Sumatera Barat https://corona.sumbarprov.go.id/
❑ DI Yogyakarta http://corona.jogjaprov.go.id/
❑ Bandung https://covid19.bandung.go.id/
❑ dll
 Indonesia vs Italia

https://www.facebook.com/photo.php?fbid=10218848789562272&set=a.1041133160064&type=3&theater
Data Science for Covid-19 Indonesia (DSCI) Initiative

DSCI hingga hari :

1) 4 Collaborators

2) 5 Datasets

3) 10 Kernels

https://www.kaggle.com/ardisragen/indonesia-coronavirus-cases
 Visualisasi Data

https://www.kaggle.com/rizkyalifr/daily-graphics-report-for-indonesia-covid-19 https://www.kaggle.com/hahasrul/novel-corona-virus-covid-19-indonesia-eda
 Visualisasi Data

https://www.kaggle.com/ardisragen/visualization-analysis-of-covid-19-in-indonesia
 Epidemic Modeling

• SIR Epidemic Model [1]

• Data Input

1. S = 26.481 orang, berdasarkan data jumlah

penduduk di Kelurahan Bangka tahun 2019 [2]
2. I = 6 orang, berdasarkan data yang ada di situs
tanggap covid-19 DKI Jakarta [3] hingga tanggal
22 Maret 2020.
3. R = 0 orang, sumber data sama dengan I.
4. alpha = (1) 1/100.000 orang untuk kasus normal,
(2), 1/125.000 orang untuk kasus dengan social
distancing.
5. T = 14 hari.

[1] https://www.maa.org/press/periodicals/loci/joma/the-sir-model-for-spread-of-disease-the-differential-equation-
model?fbclid=IwAR1ZjdRzPQq2pt2x1m6vSMrr1aUXfCtuhBLZwgA7LfuUWajYCNkV09lS87Q
[2] https://jakselkota.bps.go.id/publication/2019/09/26/dc35aaf13e766590527b64d2/kecamatan-mampang-prapatan-dalam-angka-
2019.html?fbclid=IwAR3KS6vjoat3QNbwC0VOfuB14Nv2SCoYBG1Q4tm6EmByePVSMdEiyAXpwZM
[3] https://corona.jakarta.go.id/id
Prediksi Jumlah Kasus Positif

https://www.kaggle.com/ardisragen/predicting-coronavirus-positive-cases-in-indonesia

https://www.kaggle.com/rizkyalifr/logistic-model-for-indonesia-covid-19
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